BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies.
Commun Biol
; 5(1): 151, 2022 02 22.
Article
in English
| MEDLINE | ID: covidwho-1708032
ABSTRACT
A large gap remains between sequencing a microbial community and characterizing all of the organisms inside of it. Here we develop a novel method to taxonomically bin metagenomic assemblies through alignment of contigs against a reference database. We show that this workflow, BugSplit, bins metagenome-assembled contigs to species with a 33% absolute improvement in F1-score when compared to alternative tools. We perform nanopore mNGS on patients with COVID-19, and using a reference database predating COVID-19, demonstrate that BugSplit's taxonomic binning enables sensitive and specific detection of a novel coronavirus not possible with other approaches. When applied to nanopore mNGS data from cases of Klebsiella pneumoniae and Neisseria gonorrhoeae infection, BugSplit's taxonomic binning accurately separates pathogen sequences from those of the host and microbiota, and unlocks the possibility of sequence typing, in silico serotyping, and antimicrobial resistance prediction of each organism within a sample. BugSplit is available at https//bugseq.com/academic .
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Bacteria
/
Algorithms
/
Computational Biology
/
Metagenome
/
Metagenomics
/
Nanopore Sequencing
Type of study:
Diagnostic study
/
Observational study
/
Prognostic study
Limits:
Humans
Language:
English
Journal:
Commun Biol
Year:
2022
Document Type:
Article
Affiliation country:
S42003-022-03114-4
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